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Non paired reads #31

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Non paired reads #31

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Commits on Aug 1, 2024

  1. Bug fix for running with paired=FALSE. 

    The assumption that the first value column on the `cov` object is a score column
does not hold when running fragCounter with `paired=FALSE` - see the logic in `PrepareCov`
where a different bamUtils function is used. The `count` column is set in that branch
though and is the correct column to use here.

Preserving the initial logic if `count` column does not exist though in case other
usages depend on that behavior.
    @jstimes
    jstimes committed Aug 1, 2024
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  2. Add mc.cores argument to fragCounter. 

    Passes `mc.cores` through to `PrepareCov` and then `bam.cov.gr` for
potential speed-up. With default value of 1, `bam.cov.gr` was taking
~3 days for a 116x coverage single-end PacBio reads.
    @jstimes
    jstimes committed Aug 1, 2024
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